4.User Interface

4-1.Main UI

• The image below is the main UI of Octopus-toolkit

• The description of each part are as follows.

No	Name	Description
1	Menu Bar	Functions such as Private analysis (your data).
2	Input	Input GEO accession number (GSE or GSM) or a text file containing GEO accession numbers (one GSE or GSM per line).
3	Status	brief information regarding steps and errors.
4	Open and Run	Run the anlaysis.
5	Full parameters	Setting up the parameters for each tool.
6	Progress bar	Progress bar.
7	Running information	Status window

4-2.Menu Bar

• Below are the details.

Menu	Sub Menu	Description
File	Exit	Exit the Octopus-toolkit
Analysis	Private Data	Analyze your data
	Peak Calling	Find peaks (enriched regions) for ChIP-seq MNase-seq MeDIP-seq and ATAC-seq with HOMER.
	Graph	Draw the Heatmap and Line Plot from the output.
	IGV	Visualization using IGV (Integrative Genomics Viewer)
Help	Manual(Tutorial)	Go to the Octopus-toolkit manual page.
	Error Code	Go to the Octopus-toolkit Error code page.
	Homepage	Go to the Octopus-toolkit homepage

4-3.Octopus Option

• Octopus-toolkit options

No	Name	Description
1	Main option	Main options.
2	RNA-Seq option	Options for RNA-seq data only.
3	Compression option	To save disk space.
4	Remove Files	Delete selected intermediate files after each process.

4-4.Full parameters

• The following image shows Full parameters window.

No	Name	Description
1	Analysis tree	Select one of steps
2	Paremeter window	Change parameters for the process you selected
3	Apply	You can apply or reset the option.

4-5.Private Table

You can analyze your own data (Fastq) using Octopus-toolkit (Analysis - Private Data). The private Table is a setup window for your data.

To analyze your own data, you must select appropriate information as follows.

No	Name	Description
1	Help	Go to the tutorial page.
2	Private table	Files with related information.
3	Setup	The option window is used to set appropriate information needed for processing given files.
4	Apply	You can apply or reset the option.

4-6.Peak Calling Table

You can identify peaks using the Peak Calling function. You have to select appropriate options for each file from the setting window.

This function is not applicable for RNA-seq data.

No	Name	Description
1	Help	Go to the tutorial.
2	Set up table	Parameters for peak calling
3	Files	Select files for analysis
4	Setup	Select appropriate options for given files
5	Apply	You can apply or reset the parameters

4-7.Graph Table

To draw heatmap and line plots with the identified regions.

This function is not applicable for RNA-seq data.

No	Name	Description
1	Help	Go to the tutorial.
2	Annotation	Choose a peak file.
3	Samples	Status window
4	Sample bigWig files	Select bigWig files of samples you want to draw over the identified regions in the peak file.
5	Option	Define the range (bp) relate to the center of peaks.

4-8.IGV Table

You can visualize your data with bigWig files via IGV (IGV, Integrative Genomics Viewer).

No	Name	Description
1	Help	Go to the tutorial.
2	Samples	Status window.
3	Sample bigWig files	Select bigWig files for visualization.
4	Genome	Choose the reference genome.